Passed surveys refer to those IUs that didn’t fail any impact or surveillance surveys. If no impact or surveillance surveys performed, the minimum TF prevalence was <5%.

5 categories of “problem” IUs considered throughout (not mutually exclusive):

Summarise by category

Compare baseline TF vs baseline \(\beta\)

Compare baseline TF vs effective coverage

Compare baseline TF vs effective number of MDA rounds (#rounds \(\times\) effective coverage)

Compare baseline and last TF prevalence

Compare baseline \(\beta\) and reduction in \(\beta\) by 2020

# effective MDA rounds by baseline beta and TF prev

3d plots

Beta by country

effective MDA rounds by country

logistic regression

## [1] "All IUs"
## Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
## 
## Call:
## glm(formula = passed_flag ~ ((median_beta2020 + median_reduction2020 + 
##     median_eff_mda_rounds) + baseline_tf_max + ADMIN0ISO2), family = binomial(link = "logit"), 
##     data = glm_data %>% select(-c(failed_impact_flag, persistent_flag, 
##         failed_surveillance_flag, rebound_flag, never_below_threshold_flag)))
## 
## Coefficients:
##                         Estimate Std. Error z value Pr(>|z|)    
## (Intercept)              45.6643  4928.2635   0.009   0.9926    
## median_beta2020        -235.7695    28.2860  -8.335  < 2e-16 ***
## median_reduction2020      4.5964     2.7220   1.689   0.0913 .  
## median_eff_mda_rounds    -1.2203     0.1631  -7.480 7.45e-14 ***
## baseline_tf_max0.099    -13.8726   818.4107  -0.017   0.9865    
## baseline_tf_max0.299    -11.5965   818.4108  -0.014   0.9887    
## baseline_tf_max0.499     -7.9146   818.4114  -0.010   0.9923    
## baseline_tf_max1         -7.4644   818.4134  -0.009   0.9927    
## ADMIN0ISO2BF            -17.7452  4859.8338  -0.004   0.9971    
## ADMIN0ISO2BI            -21.1779  4859.8338  -0.004   0.9965    
## ADMIN0ISO2CM            -17.8674  4859.8337  -0.004   0.9971    
## ADMIN0ISO2CF              1.8990 21228.3709   0.000   0.9999    
## ADMIN0ISO2TD            -18.2181  4859.8337  -0.004   0.9970    
## ADMIN0ISO2CG            -18.3861 17485.7854  -0.001   0.9992    
## ADMIN0ISO2CD            -17.6079  4859.8338  -0.004   0.9971    
## ADMIN0ISO2CI            -14.2583  4859.8347  -0.003   0.9977    
## ADMIN0ISO2ER            -17.8273  4859.8338  -0.004   0.9971    
## ADMIN0ISO2ET            -17.6894  4859.8337  -0.004   0.9971    
## ADMIN0ISO2GH              2.6260  5902.7056   0.000   0.9996    
## ADMIN0ISO2GN              2.0074  6489.4256   0.000   0.9998    
## ADMIN0ISO2GW            -18.1506  4859.8339  -0.004   0.9970    
## ADMIN0ISO2MW            -18.4433  4859.8338  -0.004   0.9970    
## ADMIN0ISO2ML            -20.2702  4859.8337  -0.004   0.9967    
## ADMIN0ISO2MR            -19.6458  4859.8338  -0.004   0.9968    
## ADMIN0ISO2MZ            -18.9894  4859.8337  -0.004   0.9969    
## ADMIN0ISO2NE            -21.6184  4859.8337  -0.004   0.9965    
## ADMIN0ISO2NG            -18.3850  4859.8337  -0.004   0.9970    
## ADMIN0ISO2SN            -18.4333  4859.8337  -0.004   0.9970    
## ADMIN0ISO2SS            -18.5821  4859.8346  -0.004   0.9969    
## ADMIN0ISO2TZ            -13.1264  4859.8338  -0.003   0.9978    
## ADMIN0ISO2GM              1.0477  5940.2650   0.000   0.9999    
## ADMIN0ISO2TG            -18.2597 10456.8946  -0.002   0.9986    
## ADMIN0ISO2UG            -16.8123  4859.8337  -0.003   0.9972    
## ADMIN0ISO2ZM            -19.1297  4859.8337  -0.004   0.9969    
## ADMIN0ISO2ZZ              1.0161 18371.6865   0.000   1.0000    
## ADMIN0ISO2ZW            -18.8492  4859.8338  -0.004   0.9969    
## ADMIN0ISO2KE            -18.3865  4859.8338  -0.004   0.9970    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 2679.2  on 2419  degrees of freedom
## Residual deviance:  610.5  on 2383  degrees of freedom
## AIC: 684.5
## 
## Number of Fisher Scoring iterations: 20

## [1] "Only passed and failed impact"
## Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
## 
## Call:
## glm(formula = passed_flag ~ ((median_beta2020 + median_reduction2020 + 
##     median_eff_mda_rounds) + baseline_tf_max + ADMIN0ISO2), family = binomial(link = "logit"), 
##     data = glm_data %>% filter(passed_flag == 1 | failed_impact_flag == 
##         1) %>% select(-c(failed_impact_flag, persistent_flag, 
##         failed_surveillance_flag, rebound_flag, never_below_threshold_flag)))
## 
## Coefficients:
##                         Estimate Std. Error z value Pr(>|z|)    
## (Intercept)              46.2235  4942.7505   0.009    0.993    
## median_beta2020        -311.9755    34.6013  -9.016  < 2e-16 ***
## median_reduction2020      3.4171     3.1999   1.068    0.286    
## median_eff_mda_rounds    -1.0379     0.1734  -5.985 2.16e-09 ***
## baseline_tf_max0.099    -12.7566   794.2802  -0.016    0.987    
## baseline_tf_max0.299     -9.8638   794.2804  -0.012    0.990    
## baseline_tf_max0.499     -5.4425   794.2812  -0.007    0.995    
## baseline_tf_max1         -2.8761   794.2847  -0.004    0.997    
## ADMIN0ISO2BF            -18.0770  4878.5140  -0.004    0.997    
## ADMIN0ISO2BI            -21.4811  4878.5141  -0.004    0.996    
## ADMIN0ISO2CM            -16.6010  4878.5141  -0.003    0.997    
## ADMIN0ISO2CF              1.6937 21230.7596   0.000    1.000    
## ADMIN0ISO2TD            -17.5792  4878.5140  -0.004    0.997    
## ADMIN0ISO2CG            -18.2952 17435.9689  -0.001    0.999    
## ADMIN0ISO2CD            -17.4436  4878.5141  -0.004    0.997    
## ADMIN0ISO2CI            -12.9612  4878.5172  -0.003    0.998    
## ADMIN0ISO2ER            -17.1719  4878.5141  -0.004    0.997    
## ADMIN0ISO2ET            -17.1760  4878.5140  -0.004    0.997    
## ADMIN0ISO2GH              1.7048  5931.0516   0.000    1.000    
## ADMIN0ISO2GN              2.0372  6537.1148   0.000    1.000    
## ADMIN0ISO2GW              1.6099 13848.3291   0.000    1.000    
## ADMIN0ISO2MW            -17.7923  4878.5140  -0.004    0.997    
## ADMIN0ISO2ML            -20.5255  4878.5140  -0.004    0.997    
## ADMIN0ISO2MR            -20.3533  4878.5140  -0.004    0.997    
## ADMIN0ISO2MZ            -18.3166  4878.5140  -0.004    0.997    
## ADMIN0ISO2NE            -21.7810  4878.5140  -0.004    0.996    
## ADMIN0ISO2NG            -18.2806  4878.5140  -0.004    0.997    
## ADMIN0ISO2SN            -18.6966  4878.5140  -0.004    0.997    
## ADMIN0ISO2SS            -18.9028  4878.5165  -0.004    0.997    
## ADMIN0ISO2TZ            -12.4875  4878.5141  -0.003    0.998    
## ADMIN0ISO2GM              0.2825  5960.7918   0.000    1.000    
## ADMIN0ISO2TG            -18.2153 10450.9782  -0.002    0.999    
## ADMIN0ISO2UG            -17.3657  4878.5140  -0.004    0.997    
## ADMIN0ISO2ZM            -18.7867  4878.5140  -0.004    0.997    
## ADMIN0ISO2ZZ              1.0734 18512.5759   0.000    1.000    
## ADMIN0ISO2ZW            -18.4232  4878.5141  -0.004    0.997    
## ADMIN0ISO2KE            -18.2326  4878.5140  -0.004    0.997    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 2528.03  on 2367  degrees of freedom
## Residual deviance:  476.65  on 2331  degrees of freedom
## AIC: 550.65
## 
## Number of Fisher Scoring iterations: 20

## [1] "Only passed and persistent"
## Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
## 
## Call:
## glm(formula = passed_flag ~ ((median_beta2020 + median_reduction2020 + 
##     median_eff_mda_rounds) + baseline_tf_max + ADMIN0ISO2), family = binomial(link = "logit"), 
##     data = glm_data %>% filter(passed_flag == 1 | persistent_flag == 
##         1) %>% select(-c(failed_impact_flag, persistent_flag, 
##         failed_surveillance_flag, rebound_flag, never_below_threshold_flag)))
## 
## Coefficients:
##                         Estimate Std. Error z value Pr(>|z|)    
## (Intercept)            5.322e+01  1.388e+04   0.004    0.997    
## median_beta2020       -4.837e+02  9.395e+01  -5.148 2.63e-07 ***
## median_reduction2020   1.158e+01  7.549e+00   1.534    0.125    
## median_eff_mda_rounds -3.746e-01  3.234e-01  -1.158    0.247    
## baseline_tf_max0.099  -8.366e+00  2.106e+03  -0.004    0.997    
## baseline_tf_max0.299  -5.892e+00  2.106e+03  -0.003    0.998    
## baseline_tf_max0.499   1.847e+00  2.106e+03   0.001    0.999    
## baseline_tf_max1      -1.094e+01  5.109e+03  -0.002    0.998    
## ADMIN0ISO2BF           7.158e-02  1.551e+04   0.000    1.000    
## ADMIN0ISO2BI          -3.573e+00  1.985e+04   0.000    1.000    
## ADMIN0ISO2CM           9.442e-01  1.632e+04   0.000    1.000    
## ADMIN0ISO2CF           1.901e+00  5.782e+04   0.000    1.000    
## ADMIN0ISO2TD           4.658e-03  1.655e+04   0.000    1.000    
## ADMIN0ISO2CG          -1.686e+01  4.673e+04   0.000    1.000    
## ADMIN0ISO2CD          -1.505e+00  1.482e+04   0.000    1.000    
## ADMIN0ISO2CI           6.139e-01  1.794e+04   0.000    1.000    
## ADMIN0ISO2ER           2.293e+01  1.577e+04   0.001    0.999    
## ADMIN0ISO2ET          -1.682e+01  1.372e+04  -0.001    0.999    
## ADMIN0ISO2GH          -8.930e-01  1.667e+04   0.000    1.000    
## ADMIN0ISO2GN           1.296e+00  1.881e+04   0.000    1.000    
## ADMIN0ISO2GW           1.152e+00  3.658e+04   0.000    1.000    
## ADMIN0ISO2MW           7.701e-01  2.052e+04   0.000    1.000    
## ADMIN0ISO2ML          -2.625e-01  1.609e+04   0.000    1.000    
## ADMIN0ISO2MR          -3.447e+00  1.663e+04   0.000    1.000    
## ADMIN0ISO2MZ          -1.888e+01  1.372e+04  -0.001    0.999    
## ADMIN0ISO2NE          -2.029e+01  1.372e+04  -0.001    0.999    
## ADMIN0ISO2NG          -1.742e+01  1.372e+04  -0.001    0.999    
## ADMIN0ISO2SN           6.721e-01  1.642e+04   0.000    1.000    
## ADMIN0ISO2SS          -1.720e+01  1.372e+04  -0.001    0.999    
## ADMIN0ISO2TZ          -1.296e+01  1.372e+04  -0.001    0.999    
## ADMIN0ISO2GM          -3.146e+00  1.611e+04   0.000    1.000    
## ADMIN0ISO2TG          -1.659e+01  2.849e+04  -0.001    1.000    
## ADMIN0ISO2UG           1.578e+01  1.589e+04   0.001    0.999    
## ADMIN0ISO2ZM          -1.307e+01  1.372e+04  -0.001    0.999    
## ADMIN0ISO2ZZ           9.794e-01  5.313e+04   0.000    1.000    
## ADMIN0ISO2ZW          -1.415e+00  1.940e+04   0.000    1.000    
## ADMIN0ISO2KE          -1.935e+01  1.372e+04  -0.001    0.999    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 1134.166  on 1997  degrees of freedom
## Residual deviance:   77.116  on 1961  degrees of freedom
## AIC: 151.12
## 
## Number of Fisher Scoring iterations: 22

## [1] "Only passed and failed surveillance"
## Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
## 
## Call:
## glm(formula = passed_flag ~ ((median_beta2020 + median_reduction2020 + 
##     median_eff_mda_rounds) + baseline_tf_max + ADMIN0ISO2), family = binomial(link = "logit"), 
##     data = glm_data %>% filter(passed_flag == 1 | failed_surveillance_flag == 
##         1) %>% select(-c(failed_impact_flag, persistent_flag, 
##         failed_surveillance_flag, rebound_flag, never_below_threshold_flag)))
## 
## Coefficients:
##                        Estimate Std. Error z value Pr(>|z|)    
## (Intercept)              39.087   8012.903   0.005    0.996    
## median_beta2020          61.629     48.735   1.265    0.206    
## median_reduction2020     -0.848      3.718  -0.228    0.820    
## median_eff_mda_rounds    -1.862      0.263  -7.081 1.44e-12 ***
## baseline_tf_max0.099    -16.651   1274.828  -0.013    0.990    
## baseline_tf_max0.299    -17.231   1274.828  -0.014    0.989    
## baseline_tf_max0.499    -17.412   1274.829  -0.014    0.989    
## baseline_tf_max1        -20.307   1274.832  -0.016    0.987    
## ADMIN0ISO2BF              1.200   9513.106   0.000    1.000    
## ADMIN0ISO2BI             -2.431  11993.283   0.000    1.000    
## ADMIN0ISO2CM            -18.922   7910.842  -0.002    0.998    
## ADMIN0ISO2CF              2.115  34978.450   0.000    1.000    
## ADMIN0ISO2TD            -18.178   7910.842  -0.002    0.998    
## ADMIN0ISO2CG            -17.844  28901.099  -0.001    1.000    
## ADMIN0ISO2CD             -1.801   8577.745   0.000    1.000    
## ADMIN0ISO2CI              0.387  10523.620   0.000    1.000    
## ADMIN0ISO2ER            -15.481   7910.842  -0.002    0.998    
## ADMIN0ISO2ET            -17.864   7910.842  -0.002    0.998    
## ADMIN0ISO2GH              5.612   9525.663   0.001    1.000    
## ADMIN0ISO2GN              2.077  10700.021   0.000    1.000    
## ADMIN0ISO2GW            -17.292   7910.842  -0.002    0.998    
## ADMIN0ISO2MW            -18.729   7910.842  -0.002    0.998    
## ADMIN0ISO2ML            -16.957   7910.842  -0.002    0.998    
## ADMIN0ISO2MR              1.111   9789.342   0.000    1.000    
## ADMIN0ISO2MZ            -20.172   7910.842  -0.003    0.998    
## ADMIN0ISO2NE            -19.442   7910.842  -0.002    0.998    
## ADMIN0ISO2NG            -17.161   7910.842  -0.002    0.998    
## ADMIN0ISO2SN              1.038   9622.177   0.000    1.000    
## ADMIN0ISO2SS              1.571  21591.786   0.000    1.000    
## ADMIN0ISO2TZ            -11.550   7910.842  -0.001    0.999    
## ADMIN0ISO2GM              3.326   9260.408   0.000    1.000    
## ADMIN0ISO2TG            -17.871  17208.663  -0.001    0.999    
## ADMIN0ISO2UG            -15.261   7910.842  -0.002    0.998    
## ADMIN0ISO2ZM            -18.692   7910.842  -0.002    0.998    
## ADMIN0ISO2ZZ              1.275  32004.077   0.000    1.000    
## ADMIN0ISO2ZW             -1.792  11402.869   0.000    1.000    
## ADMIN0ISO2KE            -18.589   7910.842  -0.002    0.998    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 714.65  on 1921  degrees of freedom
## Residual deviance: 282.13  on 1885  degrees of freedom
## AIC: 356.13
## 
## Number of Fisher Scoring iterations: 21

## [1] "Only passed and rebound"
## Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
## 
## Call:
## glm(formula = passed_flag ~ ((median_beta2020 + median_reduction2020 + 
##     median_eff_mda_rounds) + baseline_tf_max + ADMIN0ISO2), family = binomial(link = "logit"), 
##     data = glm_data %>% filter(passed_flag == 1 | rebound_flag == 
##         1) %>% select(-c(failed_impact_flag, persistent_flag, 
##         failed_surveillance_flag, rebound_flag, never_below_threshold_flag)))
## 
## Coefficients:
##                         Estimate Std. Error z value Pr(>|z|)    
## (Intercept)              35.9811  7952.7376   0.005  0.99639    
## median_beta2020         165.6792    63.6199   2.604  0.00921 ** 
## median_reduction2020     -3.8066     4.2987  -0.886  0.37588    
## median_eff_mda_rounds    -1.8845     0.3070  -6.139  8.3e-10 ***
## baseline_tf_max0.099    -18.5225  1268.4195  -0.015  0.98835    
## baseline_tf_max0.299    -19.5887  1268.4197  -0.015  0.98768    
## baseline_tf_max0.499    -21.6803  1268.4213  -0.017  0.98636    
## baseline_tf_max1        -26.7188  1268.4263  -0.021  0.98319    
## ADMIN0ISO2BF              1.7986  9445.0188   0.000  0.99985    
## ADMIN0ISO2BI             -1.8400 12058.2616   0.000  0.99988    
## ADMIN0ISO2CM            -19.0917  7850.9327  -0.002  0.99806    
## ADMIN0ISO2CF              2.0755 34965.3680   0.000  0.99995    
## ADMIN0ISO2TD            -17.9733  7850.9327  -0.002  0.99817    
## ADMIN0ISO2CG            -17.6400 28833.3845  -0.001  0.99951    
## ADMIN0ISO2CD             -1.6898  8517.7753   0.000  0.99984    
## ADMIN0ISO2CI              0.3987 10505.2122   0.000  0.99997    
## ADMIN0ISO2ER            -15.4350  7850.9329  -0.002  0.99843    
## ADMIN0ISO2ET            -17.5612  7850.9327  -0.002  0.99822    
## ADMIN0ISO2GH              6.0990  9516.7361   0.001  0.99949    
## ADMIN0ISO2GN              2.1558 10615.7700   0.000  0.99984    
## ADMIN0ISO2GW            -16.7579  7850.9328  -0.002  0.99830    
## ADMIN0ISO2MW            -18.5833  7850.9328  -0.002  0.99811    
## ADMIN0ISO2ML            -15.5384  7850.9328  -0.002  0.99842    
## ADMIN0ISO2MR              1.9358  9669.4953   0.000  0.99984    
## ADMIN0ISO2MZ            -19.7489  7850.9327  -0.003  0.99799    
## ADMIN0ISO2NE            -18.0776  7850.9327  -0.002  0.99816    
## ADMIN0ISO2NG            -16.9235  7850.9327  -0.002  0.99828    
## ADMIN0ISO2SN              1.3352  9473.9606   0.000  0.99989    
## ADMIN0ISO2SS              2.6349 21230.2311   0.000  0.99990    
## ADMIN0ISO2TZ            -11.2130  7850.9328  -0.001  0.99886    
## ADMIN0ISO2GM              4.3159  9311.6026   0.000  0.99963    
## ADMIN0ISO2TG            -17.7746 17170.0162  -0.001  0.99917    
## ADMIN0ISO2UG              3.3206  9375.3582   0.000  0.99972    
## ADMIN0ISO2ZM            -18.7990  7850.9327  -0.002  0.99809    
## ADMIN0ISO2ZZ              1.2928 32006.9509   0.000  0.99997    
## ADMIN0ISO2ZW             -1.3965 11330.0972   0.000  0.99990    
## ADMIN0ISO2KE            -18.1527  7850.9328  -0.002  0.99816    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 476.01  on 1885  degrees of freedom
## Residual deviance: 235.01  on 1849  degrees of freedom
## AIC: 309.01
## 
## Number of Fisher Scoring iterations: 21

## [1] "Only passed and never_below_threshold"
## Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
## 
## Call:
## glm(formula = passed_flag ~ ((median_beta2020 + median_reduction2020 + 
##     median_eff_mda_rounds) + baseline_tf_max + ADMIN0ISO2), family = binomial(link = "logit"), 
##     data = glm_data %>% filter(passed_flag == 1 | never_below_threshold_flag == 
##         1) %>% select(-c(failed_impact_flag, persistent_flag, 
##         failed_surveillance_flag, rebound_flag, never_below_threshold_flag)))
## 
## Coefficients:
##                         Estimate Std. Error z value Pr(>|z|)    
## (Intercept)            5.984e+01  1.373e+04   0.004   0.9965    
## median_beta2020       -7.271e+02  9.278e+01  -7.837 4.62e-15 ***
## median_reduction2020   1.678e+01  7.102e+00   2.363   0.0181 *  
## median_eff_mda_rounds  6.475e-03  2.484e-01   0.026   0.9792    
## baseline_tf_max0.099  -7.282e+00  2.027e+03  -0.004   0.9971    
## baseline_tf_max0.299  -5.279e-01  2.027e+03   0.000   0.9998    
## baseline_tf_max0.499   1.092e+01  2.027e+03   0.005   0.9957    
## baseline_tf_max1      -2.068e+00  4.433e+03   0.000   0.9996    
## ADMIN0ISO2BF           6.840e-02  1.503e+04   0.000   1.0000    
## ADMIN0ISO2BI          -2.893e+00  1.987e+04   0.000   0.9999    
## ADMIN0ISO2CM           9.418e-01  1.622e+04   0.000   1.0000    
## ADMIN0ISO2CF           1.230e+00  5.777e+04   0.000   1.0000    
## ADMIN0ISO2TD           5.789e-01  1.608e+04   0.000   1.0000    
## ADMIN0ISO2CG          -1.720e+01  4.534e+04   0.000   0.9997    
## ADMIN0ISO2CD          -1.794e+01  1.358e+04  -0.001   0.9989    
## ADMIN0ISO2CI          -7.720e+00  1.358e+04  -0.001   0.9995    
## ADMIN0ISO2ER           2.763e+01  1.535e+04   0.002   0.9986    
## ADMIN0ISO2ET          -1.711e+01  1.358e+04  -0.001   0.9990    
## ADMIN0ISO2GH          -2.727e+00  1.668e+04   0.000   0.9999    
## ADMIN0ISO2GN           1.375e+00  1.815e+04   0.000   0.9999    
## ADMIN0ISO2GW          -2.244e-01  3.186e+04   0.000   1.0000    
## ADMIN0ISO2MW           1.659e+00  2.036e+04   0.000   0.9999    
## ADMIN0ISO2ML          -2.437e-01  1.557e+04   0.000   1.0000    
## ADMIN0ISO2MR          -5.508e+00  1.581e+04   0.000   0.9997    
## ADMIN0ISO2MZ          -1.817e+01  1.358e+04  -0.001   0.9989    
## ADMIN0ISO2NE          -1.968e+01  1.358e+04  -0.001   0.9988    
## ADMIN0ISO2NG          -1.765e+01  1.358e+04  -0.001   0.9990    
## ADMIN0ISO2SN           5.270e-01  1.631e+04   0.000   1.0000    
## ADMIN0ISO2SS          -2.085e+01  1.358e+04  -0.002   0.9988    
## ADMIN0ISO2TZ          -1.290e+01  1.358e+04  -0.001   0.9992    
## ADMIN0ISO2GM          -3.347e+00  1.615e+04   0.000   0.9998    
## ADMIN0ISO2TG          -1.689e+01  2.818e+04  -0.001   0.9995    
## ADMIN0ISO2UG           1.784e+01  1.468e+04   0.001   0.9990    
## ADMIN0ISO2ZM          -1.926e+01  1.358e+04  -0.001   0.9989    
## ADMIN0ISO2ZZ           2.976e-01  5.271e+04   0.000   1.0000    
## ADMIN0ISO2ZW          -1.779e+01  1.358e+04  -0.001   0.9990    
## ADMIN0ISO2KE          -1.975e+01  1.358e+04  -0.001   0.9988    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 1911.33  on 2180  degrees of freedom
## Residual deviance:  124.02  on 2144  degrees of freedom
## AIC: 198.02
## 
## Number of Fisher Scoring iterations: 22

Check trajectories for IUs that failed a surveillance survey or rebounded

Legend:

## [1] "rebound not fitted"

## [1] "rebound fitted"

Check trajectories for IUs that had only baseline surveys but high prevalence

## [1] "baseline TF = 50-100%"

## [1] "baseline TF = 30-50%"

## [1] "baseline TF = 10-30%"

## [1] "baseline TF = 5-10%"